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TaKaRa ex taq dna polymerase hot start version
Sequencing electropherogram of (CA)7 . PCR of the mtDNA D-loop (CA)7 was performed using EX <t>Taq</t> <t>DNA</t> polymerase and F7/R5 primer pairs (A) or F5/R5 primer pairs (B). The sequencing electropherogram using the F5 primer is the same as (data not shown). (C) PCR was performed using a different proofreading DNA polymerase KOD and F7/R5 primer pairs. (D) PCR of genomic (CA)7 of the NAALAD2 gene was performed using EX Taq DNA polymerase. An arrow indicates a representative position used to evaluate a variant allele. PCR, polymerase chain reaction; mtDNA, mitochondrial DNA; NB, normal breast epithelia; NLN, normal lymph node; BC, breast cancer; NL16, normal liver; F, forward; R, reverse. NL16 is a different patient with a (CA)4 repeat.
Ex Taq Dna Polymerase Hot Start Version, supplied by TaKaRa, used in various techniques. Bioz Stars score: 94/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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1) Product Images from "Caution for simple sequence repeat number variation in the mitochondrial DNA D-loop to determine cancer-specific variants"

Article Title: Caution for simple sequence repeat number variation in the mitochondrial DNA D-loop to determine cancer-specific variants

Journal: Oncology Letters

doi: 10.3892/ol.2018.9809

Sequencing electropherogram of (CA)7 . PCR of the mtDNA D-loop (CA)7 was performed using EX Taq DNA polymerase and F7/R5 primer pairs (A) or F5/R5 primer pairs (B). The sequencing electropherogram using the F5 primer is the same as (data not shown). (C) PCR was performed using a different proofreading DNA polymerase KOD and F7/R5 primer pairs. (D) PCR of genomic (CA)7 of the NAALAD2 gene was performed using EX Taq DNA polymerase. An arrow indicates a representative position used to evaluate a variant allele. PCR, polymerase chain reaction; mtDNA, mitochondrial DNA; NB, normal breast epithelia; NLN, normal lymph node; BC, breast cancer; NL16, normal liver; F, forward; R, reverse. NL16 is a different patient with a (CA)4 repeat.
Figure Legend Snippet: Sequencing electropherogram of (CA)7 . PCR of the mtDNA D-loop (CA)7 was performed using EX Taq DNA polymerase and F7/R5 primer pairs (A) or F5/R5 primer pairs (B). The sequencing electropherogram using the F5 primer is the same as (data not shown). (C) PCR was performed using a different proofreading DNA polymerase KOD and F7/R5 primer pairs. (D) PCR of genomic (CA)7 of the NAALAD2 gene was performed using EX Taq DNA polymerase. An arrow indicates a representative position used to evaluate a variant allele. PCR, polymerase chain reaction; mtDNA, mitochondrial DNA; NB, normal breast epithelia; NLN, normal lymph node; BC, breast cancer; NL16, normal liver; F, forward; R, reverse. NL16 is a different patient with a (CA)4 repeat.

Techniques Used: Sequencing, Polymerase Chain Reaction, Variant Assay

Related Articles

Diagnostic Assay:

Article Title: Solitary Neurocysticercosis Case Caused by Asian Genotype of Taenia solium Confirmed by Mitochondrial DNA Analysis
Article Snippet: The PCR protocol consisted of 35 cycles of 94°C for 1 min, 60°C for 1 min, and 72°C for 2 min plus 1 cycle of 72°C for 5 min using the Ex Taq DNA polymerase Hot Start version (Takara Bio Inc., Shiga, Japan). .. In Fig. , the partial nucleotide sequence of the taeniid specimen is aligned with nucleotide sequences of cox1 from human taeniid cestodes.

Clone Assay:

Article Title: Functional characterization of Aquaporin-like genes in the human bed bug Cimex lectularius
Article Snippet: Coding sequences were amplified using primers containing restriction sites (EcoRI for ClAQP1, ClGlp1 and ClGlp2, or MfeI for ClBib for upstream primers and NheI for downstream primers) at the 5′ end. .. The clones used for full-length sequencing were used for PCR amplification by Ex Taq polymerase Hot Start Version (TaKaRa, Mountain View, CA). .. Agarose-gel purified PCR products were cloned into pJET1.2/blunt, and purified plasmids were digested by restriction enzymes.

Article Title: Squalene Cyclases and Cycloartenol Synthases from Polystichum polyblepharum and Six Allied Ferns
Article Snippet: Paragraph title: 4.2. Cloning of Squalene Cyclase cDNAs ... PCR was performed using Ex Taq DNA polymerase Hot Start Version (TaKaRa Bio, Shiga, Japan) in a final volume of 50 μL PCR conditions were identical to those reported in our previous study [ ].

Article Title: Histone deacetylase regulates insulin signaling via two pathways in pancreatic β cells
Article Snippet: For methylation-specific PCR, bisulfite-modified DNA (2 μL) was amplified in a volume of 20 μL using specific primers targeting the Irs2 gene (including the transcription factor binding sites) and 1 U of Ex Taq DNA Polymerase Hot-Start Version (TaKaRa), according to the manufacturer’s instructions. .. For direct sequencing, bisulfite-modified DNA was amplified using the primers for COBRA analysis and separated on 2.0% agarose gels.

Article Title: Color Vision Variation as Evidenced by Hybrid L/M Opsin Genes in Wild Populations of Trichromatic Alouatta New World Monkeys
Article Snippet: We carried out PCRs in volumes of 50 μl containing 1.5 units of Ex Taq polymerase hot start version (Takara Biotechnology Co., Tokyo, Japan) with 1× Ex Taq buffer, 0.2 mM dNTPs, 2.0 mM MgCl2 , 1 μM forward and reverse primers, and 5 μl of the DNA extract from feces. .. We directly sequenced both strands of the purified DNA samples using Applied Biosystems model 3130 automatic sequencer with Big Dye Terminator v3.1 Cycle Sequencing kit (Applied Biosystems Japan, Tokyo) and the PCR primers.

Article Title: Inferred L/M cone opsin polymorphism of ancestral tarsiers sheds dim light on the origin of anthropoid primates
Article Snippet: PCRs were carried out in volumes of 50 μl containing 1.5 units of Ex Taq polymerase hot start version (Takara, Tokyo, Japan) with 1× Ex Taq Buffer, 0.2 mM of dNTP, 1.5 mM MgCl2 , 1 μM of the forward and reverse primers, and ca 1 ng of the tarsier genomic DNA. .. PCRs were carried out in volumes of 50 μl containing 1.5 units of Ex Taq polymerase hot start version (Takara, Tokyo, Japan) with 1× Ex Taq Buffer, 0.2 mM of dNTP, 1.5 mM MgCl2 , 1 μM of the forward and reverse primers, and ca 1 ng of the tarsier genomic DNA.

Article Title: Life without tRNAArg-adenosine deaminase TadA: evolutionary consequences of decoding the four CGN codons as arginine in Mycoplasmas and other Mollicutes
Article Snippet: Aliquots (2 μl) of the aforementioned reaction mixtures, containing both types of primers, were incubated with 2.5 U of EX Taq DNA polymerase Hot Start version (TAKARA) in a 50 μl reaction solution, using a GeneAmp PCR System 9700 (Applied Biosystems, Life Technologies) thermal cycler. .. The cDNA amplification products were analyzed by 4% agarose (MetaPhor™ Agarose, Lonza Co.) gel electrophoresis in Tris-borate-EDTA (TBE) buffer, using 100-bp size markers (New England Biolabs) to evaluate the lengths of the PCR transcripts.

Amplification:

Article Title: Functional characterization of Aquaporin-like genes in the human bed bug Cimex lectularius
Article Snippet: Coding sequences were amplified using primers containing restriction sites (EcoRI for ClAQP1, ClGlp1 and ClGlp2, or MfeI for ClBib for upstream primers and NheI for downstream primers) at the 5′ end. .. The clones used for full-length sequencing were used for PCR amplification by Ex Taq polymerase Hot Start Version (TaKaRa, Mountain View, CA). .. Agarose-gel purified PCR products were cloned into pJET1.2/blunt, and purified plasmids were digested by restriction enzymes.

Article Title: Histone deacetylase regulates insulin signaling via two pathways in pancreatic β cells
Article Snippet: Bisulfite treatment of DNA was performed using an EpiTect Bisulfite Kit (QIAGEN) according to the manufacturer’s instructions. .. For methylation-specific PCR, bisulfite-modified DNA (2 μL) was amplified in a volume of 20 μL using specific primers targeting the Irs2 gene (including the transcription factor binding sites) and 1 U of Ex Taq DNA Polymerase Hot-Start Version (TaKaRa), according to the manufacturer’s instructions. .. The primer sequences were 5′-GGGAATTTGATAAGTGAATGG-3′ and 5′-TCCCACTAACTAACCCCAAA-3′.

Article Title: Color Vision Variation as Evidenced by Hybrid L/M Opsin Genes in Wild Populations of Trichromatic Alouatta New World Monkeys
Article Snippet: We carried out PCRs in volumes of 50 μl containing 1.5 units of Ex Taq polymerase hot start version (Takara Biotechnology Co., Tokyo, Japan) with 1× Ex Taq buffer, 0.2 mM dNTPs, 2.0 mM MgCl2 , 1 μM forward and reverse primers, and 5 μl of the DNA extract from feces. .. We set cycles at 94°C for 5 min followed by 40 cycles at 94°C for 30 s, at the annealing temperature indicated in Tables and for 30 s, and at 72°C for 30 s. Pure water was used as the template for the negative control in every reaction.

Article Title: Inferred L/M cone opsin polymorphism of ancestral tarsiers sheds dim light on the origin of anthropoid primates
Article Snippet: For each tarsier, we conducted PCR amplification and sequencing of a continuous section (approx. .. PCRs were carried out in volumes of 50 μl containing 1.5 units of Ex Taq polymerase hot start version (Takara, Tokyo, Japan) with 1× Ex Taq Buffer, 0.2 mM of dNTP, 1.5 mM MgCl2 , 1 μM of the forward and reverse primers, and ca 1 ng of the tarsier genomic DNA.

Article Title: A new species of the genus Arrup from a limestone cave in Akiyoshi-dai, Western Japan ( Chilopoda, Geophilomorpha, Mecistocephalidae)
Article Snippet: Partial sequences of 18S rRNA gene were amplified by polymerase chain reactions ( PCR ) using the primer sets, 18S-F1 and 18S-R9 ( ). .. The PCR amplification was performed in a Thermal Cycler Dice (Takara) in a 10 μl volume containing 0.5 μl of template solution, 2 mM MgCl2 , 2.5 mM each dNTP, 10 pmol each primer, and 0.25 U Ex Taq polymerase Hot Start version (Takara) in 1× buffer provided by the manufacturer. .. Amplification conditions were 95 °C for 2 min; 35 cycles of 95 °C for 30 sec, 50 °C for 30 sec, and 72 °C for 2 min; and 72 °C for 7 min. Amplification products were purified with the ExoSAP-IT kit (Thermo Fisher Scientific).

Article Title: Gene conversion and purifying selection shape nucleotide variation in gibbon L/M opsin genes
Article Snippet: By using the combination of these two PCR sets, we avoided the possible misinterpretation of the presence or absence of a gene type by false-positive or false-negative amplification by the gene-specific primers. .. PCRs were carried out in 25 μl containing 1.5 units of Ex Taq polymerase hot start version (Takara, Tokyo) with 1× Ex Taq Buffer, 0.2 mM each of dNTPs, 1 μM each of the forward and reverse primers, and ca.

Article Title: Life without tRNAArg-adenosine deaminase TadA: evolutionary consequences of decoding the four CGN codons as arginine in Mycoplasmas and other Mollicutes
Article Snippet: In addition to the first strand cDNA synthesis primers, the following primers 5′-GCCCG-TAGAT-CAATT-GGATA-GATCG-CTTGA-3′ (Mca-2nd) and 5′-GCCCG-TAGCT-CAATG-GATAG-AGCGT-TTGA-3′ (Bsu-2nd) were used for further polymerase chain reaction (PCR) amplification of the cDNAs (gray arrows in A). .. Aliquots (2 μl) of the aforementioned reaction mixtures, containing both types of primers, were incubated with 2.5 U of EX Taq DNA polymerase Hot Start version (TAKARA) in a 50 μl reaction solution, using a GeneAmp PCR System 9700 (Applied Biosystems, Life Technologies) thermal cycler.

Article Title: Raspberry Ketone Promotes the Differentiation of C3H10T1/2 Stem Cells into Osteoblasts
Article Snippet: A total of 1 μ g of RNA-treated DNase I (Sigma) was reverse transcribed to cDNA using the Transcriptor First-Strand cDNA Synthesis Kit (Roche, Indianapolis, IN, USA). .. One microliter of the product was used for polymerase chain reaction (PCR) amplification in a total volume of 25 μ L containing 1× Taq reaction buffer, 0.2 mM dNTPs, 2 mM MgCl2 , 1 μ M of each primer, and 0.5 U of Takara Ex Taq ® polymerase Hot Start Version (Takara, Otsu, Japan). .. The primers for α 1(I) collagen, osteocalcin, transforming growth factor β s (TGF- β 1, TGF- β 2, and TGF- β 3), and BMP-2 were synthesized by referring to already published articles., β -Actin was used as the housekeeping gene as an endogenous control.

Article Title: Solitary Neurocysticercosis Case Caused by Asian Genotype of Taenia solium Confirmed by Mitochondrial DNA Analysis
Article Snippet: Two products, one of approximately 1.6 kb and one of 984 bp, were successfully amplified by using 5′-TTGTTATAAATTTTTGATTACTAAC-3′ ( ) as the forward primer and 5′-TCCACTAAGCATAATGCAAAAGGC-3′ ( ) and 5′-GACATAACATAATGAAAATG-3′, respectively, as the reverse primers (reference and data not shown). .. The PCR protocol consisted of 35 cycles of 94°C for 1 min, 60°C for 1 min, and 72°C for 2 min plus 1 cycle of 72°C for 5 min using the Ex Taq DNA polymerase Hot Start version (Takara Bio Inc., Shiga, Japan).

Positive Control:

Article Title: Polymorphism-specific PCR enhances the diagnostic performance of American tegumentary leishmaniasis and allows the rapid identification of Leishmania species from Argentina
Article Snippet: DNA extracted from Leishmania promastigotes cultured in vitro or from confirmed ATL patients was used as a positive control, whereas DNA of eight healthy individuals from non-endemic area (Japanese subjects) or from lesions of non-ATL patients was used as negative control. .. Additional experiments to control the DNA preparation procedure, as well as to detect the presence of PCR inhibitors were performed using the TaKaRa Ex Taq DNA polymerase Hot Start Version (Takara-Bio, Shiga, Japan) and specific primers for the human glyceraldehydes 3-phosphate dehydrogenase (GAPDH ) gene, following a previously reported protocol [ ].

Synthesized:

Article Title: Functional characterization of Aquaporin-like genes in the human bed bug Cimex lectularius
Article Snippet: The clones used for full-length sequencing were used for PCR amplification by Ex Taq polymerase Hot Start Version (TaKaRa, Mountain View, CA). .. Purified constructs were linearized by XbaI for in vitro complementary RNA (cRNA) transcription with T3 RNA polymerase (Agilent Technologies, Inc., Santa Clara, CA).

Article Title: The positive feedback loop between ILF3 and lncRNA ILF3-AS1 promotes melanoma proliferation, migration, and invasion
Article Snippet: The complementary DNA encoding ILF3 was PCR-amplified by the Ex Taq DNA polymerase hot-start version (Takara) and subcloned into the Nhe I and Kpn I sites of pcDNA3.1(+) plasmid (Thermo Fisher Scientific). .. The empty plasmid pcDNA3.1(+) was used as negative control.

TA Cloning:

Article Title: Histone deacetylase regulates insulin signaling via two pathways in pancreatic β cells
Article Snippet: For methylation-specific PCR, bisulfite-modified DNA (2 μL) was amplified in a volume of 20 μL using specific primers targeting the Irs2 gene (including the transcription factor binding sites) and 1 U of Ex Taq DNA Polymerase Hot-Start Version (TaKaRa), according to the manufacturer’s instructions. .. For direct sequencing, bisulfite-modified DNA was amplified using the primers for COBRA analysis and separated on 2.0% agarose gels.

Construct:

Article Title: Functional characterization of Aquaporin-like genes in the human bed bug Cimex lectularius
Article Snippet: The clones used for full-length sequencing were used for PCR amplification by Ex Taq polymerase Hot Start Version (TaKaRa, Mountain View, CA). .. The clones used for full-length sequencing were used for PCR amplification by Ex Taq polymerase Hot Start Version (TaKaRa, Mountain View, CA).

Electrophoresis:

Article Title: Gene conversion and purifying selection shape nucleotide variation in gibbon L/M opsin genes
Article Snippet: PCRs were carried out in 25 μl containing 1.5 units of Ex Taq polymerase hot start version (Takara, Tokyo) with 1× Ex Taq Buffer, 0.2 mM each of dNTPs, 1 μM each of the forward and reverse primers, and ca. .. 5 ng of the gibbon genomic DNA at 94°C for 10 min followed by 35 cycles at 94°C for 30 sec, 65°C for 30 sec, and 72°C for 4 min. Distilled water was used as the template for the negative control in every reaction.

Incubation:

Article Title: Life without tRNAArg-adenosine deaminase TadA: evolutionary consequences of decoding the four CGN codons as arginine in Mycoplasmas and other Mollicutes
Article Snippet: In addition to the first strand cDNA synthesis primers, the following primers 5′-GCCCG-TAGAT-CAATT-GGATA-GATCG-CTTGA-3′ (Mca-2nd) and 5′-GCCCG-TAGCT-CAATG-GATAG-AGCGT-TTGA-3′ (Bsu-2nd) were used for further polymerase chain reaction (PCR) amplification of the cDNAs (gray arrows in A). .. Aliquots (2 μl) of the aforementioned reaction mixtures, containing both types of primers, were incubated with 2.5 U of EX Taq DNA polymerase Hot Start version (TAKARA) in a 50 μl reaction solution, using a GeneAmp PCR System 9700 (Applied Biosystems, Life Technologies) thermal cycler. .. The final concentrations of primers and dNTPs were 400 nM and 200 μM (each), respectively.

Formalin-fixed Paraffin-Embedded:

Article Title: Solitary Neurocysticercosis Case Caused by Asian Genotype of Taenia solium Confirmed by Mitochondrial DNA Analysis
Article Snippet: For definitive diagnosis of the causative agent, mitochondrial DNA analysis was performed using a small piece of a formalin-fixed, paraffin-embedded specimen. .. The PCR protocol consisted of 35 cycles of 94°C for 1 min, 60°C for 1 min, and 72°C for 2 min plus 1 cycle of 72°C for 5 min using the Ex Taq DNA polymerase Hot Start version (Takara Bio Inc., Shiga, Japan).

Expressing:

Article Title: Functional characterization of Aquaporin-like genes in the human bed bug Cimex lectularius
Article Snippet: Paragraph title: Cloning, expression in Xenopus oocytes, and swelling assays ... The clones used for full-length sequencing were used for PCR amplification by Ex Taq polymerase Hot Start Version (TaKaRa, Mountain View, CA).

Article Title: The positive feedback loop between ILF3 and lncRNA ILF3-AS1 promotes melanoma proliferation, migration, and invasion
Article Snippet: The complementary DNA encoding ILF3 was PCR-amplified by the Ex Taq DNA polymerase hot-start version (Takara) and subcloned into the Nhe I and Kpn I sites of pcDNA3.1(+) plasmid (Thermo Fisher Scientific). .. The empty plasmid pcDNA3.1(+) was used as negative control.

Modification:

Article Title: Histone deacetylase regulates insulin signaling via two pathways in pancreatic β cells
Article Snippet: Paragraph title: DNA bisulfite modification, combined bisulfite restriction analysis (COBRA), and direct sequencing ... For methylation-specific PCR, bisulfite-modified DNA (2 μL) was amplified in a volume of 20 μL using specific primers targeting the Irs2 gene (including the transcription factor binding sites) and 1 U of Ex Taq DNA Polymerase Hot-Start Version (TaKaRa), according to the manufacturer’s instructions.

Western Blot:

Article Title: Solitary Neurocysticercosis Case Caused by Asian Genotype of Taenia solium Confirmed by Mitochondrial DNA Analysis
Article Snippet: Serological confirmation of immunoblots using both purified glycoproteins ( ) and a recombinant chimeric antigen ( ) was carried out at Asahikawa Medical College before surgical operation; however, there was no detectable specific antibody response against either antigen (data not shown). .. The PCR protocol consisted of 35 cycles of 94°C for 1 min, 60°C for 1 min, and 72°C for 2 min plus 1 cycle of 72°C for 5 min using the Ex Taq DNA polymerase Hot Start version (Takara Bio Inc., Shiga, Japan).

Transformation Assay:

Article Title: Squalene Cyclases and Cycloartenol Synthases from Polystichum polyblepharum and Six Allied Ferns
Article Snippet: PCR was performed using Ex Taq DNA polymerase Hot Start Version (TaKaRa Bio, Shiga, Japan) in a final volume of 50 μL PCR conditions were identical to those reported in our previous study [ ]. .. The primer-specific amplicon was purified from an agarose gel, cloned into pT7 Blue T-Vector (Merck KGaA, Darmstadt, Germany), and transformed into E. coli strain DH5α.

Transfection:

Article Title: The positive feedback loop between ILF3 and lncRNA ILF3-AS1 promotes melanoma proliferation, migration, and invasion
Article Snippet: Paragraph title: Plasmids’ construction and transfection ... The complementary DNA encoding ILF3 was PCR-amplified by the Ex Taq DNA polymerase hot-start version (Takara) and subcloned into the Nhe I and Kpn I sites of pcDNA3.1(+) plasmid (Thermo Fisher Scientific).

Cell Culture:

Article Title: Polymorphism-specific PCR enhances the diagnostic performance of American tegumentary leishmaniasis and allows the rapid identification of Leishmania species from Argentina
Article Snippet: DNA extracted from Leishmania promastigotes cultured in vitro or from confirmed ATL patients was used as a positive control, whereas DNA of eight healthy individuals from non-endemic area (Japanese subjects) or from lesions of non-ATL patients was used as negative control. .. Additional experiments to control the DNA preparation procedure, as well as to detect the presence of PCR inhibitors were performed using the TaKaRa Ex Taq DNA polymerase Hot Start Version (Takara-Bio, Shiga, Japan) and specific primers for the human glyceraldehydes 3-phosphate dehydrogenase (GAPDH ) gene, following a previously reported protocol [ ].

Polymerase Chain Reaction:

Article Title: Caution for simple sequence repeat number variation in the mitochondrial DNA D-loop to determine cancer-specific variants
Article Snippet: The use of tumor and adjacent non-tumor tissues from the resected specimens to this study was approved by the Ethics Committee of Nihon University School of Medicine (approval nos. .. PCR was performed in 20-µl reactions using Takara EX Taq DNA polymerase Hot Start Version (Takara Bio Inc., Shiga, Japan) and KOD-Plus-Neo (Toyobo, Osaka, Japan) according to the manufacturer's instructions. .. The former is a mixture of recombinant Taq DNA polymerase and 3′-5′ exonuclease, and the latter is an enzyme possessing 3′-5′ exonuclease activity; this enzyme is derived from the KOD1 strain of Thermococcus kodakaraensis and as described in the manufacturer's instructions, has 80-fold fidelity compared to recombinant Taq DNA polymerase.

Article Title: Functional characterization of Aquaporin-like genes in the human bed bug Cimex lectularius
Article Snippet: Coding sequences were amplified using primers containing restriction sites (EcoRI for ClAQP1, ClGlp1 and ClGlp2, or MfeI for ClBib for upstream primers and NheI for downstream primers) at the 5′ end. .. The clones used for full-length sequencing were used for PCR amplification by Ex Taq polymerase Hot Start Version (TaKaRa, Mountain View, CA). .. Agarose-gel purified PCR products were cloned into pJET1.2/blunt, and purified plasmids were digested by restriction enzymes.

Article Title: Squalene Cyclases and Cycloartenol Synthases from Polystichum polyblepharum and Six Allied Ferns
Article Snippet: Homology-based nested PCR was performed using the single-strand cDNA and five degenerate primers [ , ] (SC-306S-1, SC-306S-2, SC-358S, SC-494A, and SC-537A). .. PCR was performed using Ex Taq DNA polymerase Hot Start Version (TaKaRa Bio, Shiga, Japan) in a final volume of 50 μL PCR conditions were identical to those reported in our previous study [ ]. .. The primer-specific amplicon was purified from an agarose gel, cloned into pT7 Blue T-Vector (Merck KGaA, Darmstadt, Germany), and transformed into E. coli strain DH5α.

Article Title: The positive feedback loop between ILF3 and lncRNA ILF3-AS1 promotes melanoma proliferation, migration, and invasion
Article Snippet: After three times of washes, the membranes were incubated with horseradish peroxidase-conjugated goat antimouse or goat antirabbit secondary antibody (Abcam) and detected using the enhanced chemiluminescence. .. The complementary DNA encoding ILF3 was PCR-amplified by the Ex Taq DNA polymerase hot-start version (Takara) and subcloned into the Nhe I and Kpn I sites of pcDNA3.1(+) plasmid (Thermo Fisher Scientific). .. The sequences of primers were as follows: 5′-CTAGCTAGCGATAAGCAAAAGTTTGATTTCCAG-3′ (sense) and 5′-GGGGTACCGGAGTAAGTGCAGAAGGTAGA-3′ (anti-sense).

Article Title: Histone deacetylase regulates insulin signaling via two pathways in pancreatic β cells
Article Snippet: Bisulfite treatment of DNA was performed using an EpiTect Bisulfite Kit (QIAGEN) according to the manufacturer’s instructions. .. For methylation-specific PCR, bisulfite-modified DNA (2 μL) was amplified in a volume of 20 μL using specific primers targeting the Irs2 gene (including the transcription factor binding sites) and 1 U of Ex Taq DNA Polymerase Hot-Start Version (TaKaRa), according to the manufacturer’s instructions. .. The primer sequences were 5′-GGGAATTTGATAAGTGAATGG-3′ and 5′-TCCCACTAACTAACCCCAAA-3′.

Article Title: Color Vision Variation as Evidenced by Hybrid L/M Opsin Genes in Wild Populations of Trichromatic Alouatta New World Monkeys
Article Snippet: We designed PCR primers to obtain both L and M opsin sequences simultaneously as we did with the exon PCRs. .. We carried out PCRs in volumes of 50 μl containing 1.5 units of Ex Taq polymerase hot start version (Takara Biotechnology Co., Tokyo, Japan) with 1× Ex Taq buffer, 0.2 mM dNTPs, 2.0 mM MgCl2 , 1 μM forward and reverse primers, and 5 μl of the DNA extract from feces.

Article Title: Inferred L/M cone opsin polymorphism of ancestral tarsiers sheds dim light on the origin of anthropoid primates
Article Snippet: PCR primers were designed to amplify overlapping segments in this region based on conservation of nucleotide sequences among previously reported L/M opsin genes of other primates (see the electronic supplementary material, figure S2). .. PCRs were carried out in volumes of 50 μl containing 1.5 units of Ex Taq polymerase hot start version (Takara, Tokyo, Japan) with 1× Ex Taq Buffer, 0.2 mM of dNTP, 1.5 mM MgCl2 , 1 μM of the forward and reverse primers, and ca 1 ng of the tarsier genomic DNA.

Article Title: Polymorphism-specific PCR enhances the diagnostic performance of American tegumentary leishmaniasis and allows the rapid identification of Leishmania species from Argentina
Article Snippet: DNA extracted from Leishmania promastigotes cultured in vitro or from confirmed ATL patients was used as a positive control, whereas DNA of eight healthy individuals from non-endemic area (Japanese subjects) or from lesions of non-ATL patients was used as negative control. .. Additional experiments to control the DNA preparation procedure, as well as to detect the presence of PCR inhibitors were performed using the TaKaRa Ex Taq DNA polymerase Hot Start Version (Takara-Bio, Shiga, Japan) and specific primers for the human glyceraldehydes 3-phosphate dehydrogenase (GAPDH ) gene, following a previously reported protocol [ ]. .. The PCR products were separated in agarose gels containing ethidium bromide, visualized under UV light and the results were recorded with a Kodak EDAS 290 gel documentation system (Kodak, Rochester, NY).

Article Title: A new species of the genus Arrup from a limestone cave in Akiyoshi-dai, Western Japan ( Chilopoda, Geophilomorpha, Mecistocephalidae)
Article Snippet: Partial sequences of 18S rRNA gene were amplified by polymerase chain reactions ( PCR ) using the primer sets, 18S-F1 and 18S-R9 ( ). .. The PCR amplification was performed in a Thermal Cycler Dice (Takara) in a 10 μl volume containing 0.5 μl of template solution, 2 mM MgCl2 , 2.5 mM each dNTP, 10 pmol each primer, and 0.25 U Ex Taq polymerase Hot Start version (Takara) in 1× buffer provided by the manufacturer. .. Amplification conditions were 95 °C for 2 min; 35 cycles of 95 °C for 30 sec, 50 °C for 30 sec, and 72 °C for 2 min; and 72 °C for 7 min. Amplification products were purified with the ExoSAP-IT kit (Thermo Fisher Scientific).

Article Title: Gene conversion and purifying selection shape nucleotide variation in gibbon L/M opsin genes
Article Snippet: This is an improvement from previous studies relying on the success of PCR using gene-specific primers [ , ]. .. PCRs were carried out in 25 μl containing 1.5 units of Ex Taq polymerase hot start version (Takara, Tokyo) with 1× Ex Taq Buffer, 0.2 mM each of dNTPs, 1 μM each of the forward and reverse primers, and ca.

Article Title: Life without tRNAArg-adenosine deaminase TadA: evolutionary consequences of decoding the four CGN codons as arginine in Mycoplasmas and other Mollicutes
Article Snippet: In addition to the first strand cDNA synthesis primers, the following primers 5′-GCCCG-TAGAT-CAATT-GGATA-GATCG-CTTGA-3′ (Mca-2nd) and 5′-GCCCG-TAGCT-CAATG-GATAG-AGCGT-TTGA-3′ (Bsu-2nd) were used for further polymerase chain reaction (PCR) amplification of the cDNAs (gray arrows in A). .. Aliquots (2 μl) of the aforementioned reaction mixtures, containing both types of primers, were incubated with 2.5 U of EX Taq DNA polymerase Hot Start version (TAKARA) in a 50 μl reaction solution, using a GeneAmp PCR System 9700 (Applied Biosystems, Life Technologies) thermal cycler. .. The final concentrations of primers and dNTPs were 400 nM and 200 μM (each), respectively.

Article Title: Changes in Variable Number of Tandem Repeats in ‘Candidatus Liberibacter asiaticus’ through Insect Transmission
Article Snippet: Additionally, another forward primer was designed in order to be easy to count the motif of VNTR ‘001’ by using a program available on the Primer3 website ( http://frodo.wi.mit.edu/primer3/ ) ( ). .. PCR was performed using a GeneAmp PCR System 9700 (Applied Biosystems, Foster City, CA, USA) in a 20-μL reaction mixture containing 1 μL of DNA template, 0.1 μM of each primer, 200 μM dNTP mixture, 1× PCR buffer, and 2.5 units of Ex Taq DNA polymerase Hot Start Version (TaKaRa, Shiga, Japan). .. The thermal cycling conditions were as follows: initial denaturation at 92°C for 2 min; 35 cycles of denaturing at 92°C for 30 s, annealing at 54°C for 30 s, and extension at 72°C for 1 min. Amplified PCR products were separated by electrophoresis in a 1.5% (wt/vol) agarose gel in Tris-boric acid EDTA buffer.

Article Title: Unique Features of a Japanese ‘Candidatus Liberibacter asiaticus’ Strain Revealed by Whole Genome Sequencing
Article Snippet: Other primers were selected from Duan et al. . .. PCR was performed with the Gene Amp PCR System 9700 (Applied Biosystems, Foster City, CA) in 20-µl reactions containing 1 µl DNA template, 0.1 µM each primer, 200 µM dNTPs, 1× PCR buffer, and 2.5 units of Ex Taq DNA polymerase Hot Start Version (TaKaRa, Shiga, Japan) under the following cycling conditions: initial denaturation at 92°C for 2 min; 35 cycles of denaturation at 92°C for 30 s, annealing at 54°C for 30 s, and extension for 1 min/kb of the desired product at 72°C. .. Long-range PCR of products above 3.0 kbp was performed with Tks Gflex DNA polymerase (TaKaRa).

Article Title: Raspberry Ketone Promotes the Differentiation of C3H10T1/2 Stem Cells into Osteoblasts
Article Snippet: A total of 1 μ g of RNA-treated DNase I (Sigma) was reverse transcribed to cDNA using the Transcriptor First-Strand cDNA Synthesis Kit (Roche, Indianapolis, IN, USA). .. One microliter of the product was used for polymerase chain reaction (PCR) amplification in a total volume of 25 μ L containing 1× Taq reaction buffer, 0.2 mM dNTPs, 2 mM MgCl2 , 1 μ M of each primer, and 0.5 U of Takara Ex Taq ® polymerase Hot Start Version (Takara, Otsu, Japan). .. The primers for α 1(I) collagen, osteocalcin, transforming growth factor β s (TGF- β 1, TGF- β 2, and TGF- β 3), and BMP-2 were synthesized by referring to already published articles., β -Actin was used as the housekeeping gene as an endogenous control.

Article Title: Solitary Neurocysticercosis Case Caused by Asian Genotype of Taenia solium Confirmed by Mitochondrial DNA Analysis
Article Snippet: Two products, one of approximately 1.6 kb and one of 984 bp, were successfully amplified by using 5′-TTGTTATAAATTTTTGATTACTAAC-3′ ( ) as the forward primer and 5′-TCCACTAAGCATAATGCAAAAGGC-3′ ( ) and 5′-GACATAACATAATGAAAATG-3′, respectively, as the reverse primers (reference and data not shown). .. The PCR protocol consisted of 35 cycles of 94°C for 1 min, 60°C for 1 min, and 72°C for 2 min plus 1 cycle of 72°C for 5 min using the Ex Taq DNA polymerase Hot Start version (Takara Bio Inc., Shiga, Japan). .. The samples for DNA sequencing were prepared using the ABI PRISM BigDye Terminator Cycle Sequencing Ready Reaction kit, and DNA sequencing was performed on an ABI PRISM 310 Genetic Analyzer.

Sequencing:

Article Title: Caution for simple sequence repeat number variation in the mitochondrial DNA D-loop to determine cancer-specific variants
Article Snippet: PCR was performed in 20-µl reactions using Takara EX Taq DNA polymerase Hot Start Version (Takara Bio Inc., Shiga, Japan) and KOD-Plus-Neo (Toyobo, Osaka, Japan) according to the manufacturer's instructions. .. PCR was performed in 20-µl reactions using Takara EX Taq DNA polymerase Hot Start Version (Takara Bio Inc., Shiga, Japan) and KOD-Plus-Neo (Toyobo, Osaka, Japan) according to the manufacturer's instructions.

Article Title: Functional characterization of Aquaporin-like genes in the human bed bug Cimex lectularius
Article Snippet: Coding sequences were amplified using primers containing restriction sites (EcoRI for ClAQP1, ClGlp1 and ClGlp2, or MfeI for ClBib for upstream primers and NheI for downstream primers) at the 5′ end. .. The clones used for full-length sequencing were used for PCR amplification by Ex Taq polymerase Hot Start Version (TaKaRa, Mountain View, CA). .. Agarose-gel purified PCR products were cloned into pJET1.2/blunt, and purified plasmids were digested by restriction enzymes.

Article Title: Squalene Cyclases and Cycloartenol Synthases from Polystichum polyblepharum and Six Allied Ferns
Article Snippet: PCR was performed using Ex Taq DNA polymerase Hot Start Version (TaKaRa Bio, Shiga, Japan) in a final volume of 50 μL PCR conditions were identical to those reported in our previous study [ ]. .. PCR was performed using Ex Taq DNA polymerase Hot Start Version (TaKaRa Bio, Shiga, Japan) in a final volume of 50 μL PCR conditions were identical to those reported in our previous study [ ].

Article Title: Histone deacetylase regulates insulin signaling via two pathways in pancreatic β cells
Article Snippet: Paragraph title: DNA bisulfite modification, combined bisulfite restriction analysis (COBRA), and direct sequencing ... For methylation-specific PCR, bisulfite-modified DNA (2 μL) was amplified in a volume of 20 μL using specific primers targeting the Irs2 gene (including the transcription factor binding sites) and 1 U of Ex Taq DNA Polymerase Hot-Start Version (TaKaRa), according to the manufacturer’s instructions.

Article Title: Color Vision Variation as Evidenced by Hybrid L/M Opsin Genes in Wild Populations of Trichromatic Alouatta New World Monkeys
Article Snippet: Paragraph title: Determination of Entire Coding Sequence of L/M Opsin Genes ... We carried out PCRs in volumes of 50 μl containing 1.5 units of Ex Taq polymerase hot start version (Takara Biotechnology Co., Tokyo, Japan) with 1× Ex Taq buffer, 0.2 mM dNTPs, 2.0 mM MgCl2 , 1 μM forward and reverse primers, and 5 μl of the DNA extract from feces.

Article Title: Inferred L/M cone opsin polymorphism of ancestral tarsiers sheds dim light on the origin of anthropoid primates
Article Snippet: For each tarsier, we conducted PCR amplification and sequencing of a continuous section (approx. .. PCRs were carried out in volumes of 50 μl containing 1.5 units of Ex Taq polymerase hot start version (Takara, Tokyo, Japan) with 1× Ex Taq Buffer, 0.2 mM of dNTP, 1.5 mM MgCl2 , 1 μM of the forward and reverse primers, and ca 1 ng of the tarsier genomic DNA.

Article Title: A new species of the genus Arrup from a limestone cave in Akiyoshi-dai, Western Japan ( Chilopoda, Geophilomorpha, Mecistocephalidae)
Article Snippet: The PCR amplification was performed in a Thermal Cycler Dice (Takara) in a 10 μl volume containing 0.5 μl of template solution, 2 mM MgCl2 , 2.5 mM each dNTP, 10 pmol each primer, and 0.25 U Ex Taq polymerase Hot Start version (Takara) in 1× buffer provided by the manufacturer. .. The PCR amplification was performed in a Thermal Cycler Dice (Takara) in a 10 μl volume containing 0.5 μl of template solution, 2 mM MgCl2 , 2.5 mM each dNTP, 10 pmol each primer, and 0.25 U Ex Taq polymerase Hot Start version (Takara) in 1× buffer provided by the manufacturer.

Article Title: Gene conversion and purifying selection shape nucleotide variation in gibbon L/M opsin genes
Article Snippet: Paragraph title: Genotyping and sequencing of the gibbon L and M opsin genes ... PCRs were carried out in 25 μl containing 1.5 units of Ex Taq polymerase hot start version (Takara, Tokyo) with 1× Ex Taq Buffer, 0.2 mM each of dNTPs, 1 μM each of the forward and reverse primers, and ca.

Article Title: Life without tRNAArg-adenosine deaminase TadA: evolutionary consequences of decoding the four CGN codons as arginine in Mycoplasmas and other Mollicutes
Article Snippet: Aliquots (2 μl) of the aforementioned reaction mixtures, containing both types of primers, were incubated with 2.5 U of EX Taq DNA polymerase Hot Start version (TAKARA) in a 50 μl reaction solution, using a GeneAmp PCR System 9700 (Applied Biosystems, Life Technologies) thermal cycler. .. Aliquots (2 μl) of the aforementioned reaction mixtures, containing both types of primers, were incubated with 2.5 U of EX Taq DNA polymerase Hot Start version (TAKARA) in a 50 μl reaction solution, using a GeneAmp PCR System 9700 (Applied Biosystems, Life Technologies) thermal cycler.

Article Title: Changes in Variable Number of Tandem Repeats in ‘Candidatus Liberibacter asiaticus’ through Insect Transmission
Article Snippet: PCR was performed using a GeneAmp PCR System 9700 (Applied Biosystems, Foster City, CA, USA) in a 20-μL reaction mixture containing 1 μL of DNA template, 0.1 μM of each primer, 200 μM dNTP mixture, 1× PCR buffer, and 2.5 units of Ex Taq DNA polymerase Hot Start Version (TaKaRa, Shiga, Japan). .. The thermal cycling conditions were as follows: initial denaturation at 92°C for 2 min; 35 cycles of denaturing at 92°C for 30 s, annealing at 54°C for 30 s, and extension at 72°C for 1 min. Amplified PCR products were separated by electrophoresis in a 1.5% (wt/vol) agarose gel in Tris-boric acid EDTA buffer.

Article Title: Unique Features of a Japanese ‘Candidatus Liberibacter asiaticus’ Strain Revealed by Whole Genome Sequencing
Article Snippet: Many In/Dels and SNPs were found by mapping the sequence reads of Ishi-1 to the complete sequence of the pathogenic ‘Ca. .. PCR was performed with the Gene Amp PCR System 9700 (Applied Biosystems, Foster City, CA) in 20-µl reactions containing 1 µl DNA template, 0.1 µM each primer, 200 µM dNTPs, 1× PCR buffer, and 2.5 units of Ex Taq DNA polymerase Hot Start Version (TaKaRa, Shiga, Japan) under the following cycling conditions: initial denaturation at 92°C for 2 min; 35 cycles of denaturation at 92°C for 30 s, annealing at 54°C for 30 s, and extension for 1 min/kb of the desired product at 72°C.

Article Title: Solitary Neurocysticercosis Case Caused by Asian Genotype of Taenia solium Confirmed by Mitochondrial DNA Analysis
Article Snippet: The PCR protocol consisted of 35 cycles of 94°C for 1 min, 60°C for 1 min, and 72°C for 2 min plus 1 cycle of 72°C for 5 min using the Ex Taq DNA polymerase Hot Start version (Takara Bio Inc., Shiga, Japan). .. The samples for DNA sequencing were prepared using the ABI PRISM BigDye Terminator Cycle Sequencing Ready Reaction kit, and DNA sequencing was performed on an ABI PRISM 310 Genetic Analyzer.

Binding Assay:

Article Title: Histone deacetylase regulates insulin signaling via two pathways in pancreatic β cells
Article Snippet: Bisulfite treatment of DNA was performed using an EpiTect Bisulfite Kit (QIAGEN) according to the manufacturer’s instructions. .. For methylation-specific PCR, bisulfite-modified DNA (2 μL) was amplified in a volume of 20 μL using specific primers targeting the Irs2 gene (including the transcription factor binding sites) and 1 U of Ex Taq DNA Polymerase Hot-Start Version (TaKaRa), according to the manufacturer’s instructions. .. The primer sequences were 5′-GGGAATTTGATAAGTGAATGG-3′ and 5′-TCCCACTAACTAACCCCAAA-3′.

Staining:

Article Title: Histone deacetylase regulates insulin signaling via two pathways in pancreatic β cells
Article Snippet: For methylation-specific PCR, bisulfite-modified DNA (2 μL) was amplified in a volume of 20 μL using specific primers targeting the Irs2 gene (including the transcription factor binding sites) and 1 U of Ex Taq DNA Polymerase Hot-Start Version (TaKaRa), according to the manufacturer’s instructions. .. For methylation-specific PCR, bisulfite-modified DNA (2 μL) was amplified in a volume of 20 μL using specific primers targeting the Irs2 gene (including the transcription factor binding sites) and 1 U of Ex Taq DNA Polymerase Hot-Start Version (TaKaRa), according to the manufacturer’s instructions.

Article Title: Raspberry Ketone Promotes the Differentiation of C3H10T1/2 Stem Cells into Osteoblasts
Article Snippet: One microliter of the product was used for polymerase chain reaction (PCR) amplification in a total volume of 25 μ L containing 1× Taq reaction buffer, 0.2 mM dNTPs, 2 mM MgCl2 , 1 μ M of each primer, and 0.5 U of Takara Ex Taq ® polymerase Hot Start Version (Takara, Otsu, Japan). .. The primers for α 1(I) collagen, osteocalcin, transforming growth factor β s (TGF- β 1, TGF- β 2, and TGF- β 3), and BMP-2 were synthesized by referring to already published articles., β -Actin was used as the housekeeping gene as an endogenous control.

Nucleic Acid Electrophoresis:

Article Title: Life without tRNAArg-adenosine deaminase TadA: evolutionary consequences of decoding the four CGN codons as arginine in Mycoplasmas and other Mollicutes
Article Snippet: Aliquots (2 μl) of the aforementioned reaction mixtures, containing both types of primers, were incubated with 2.5 U of EX Taq DNA polymerase Hot Start version (TAKARA) in a 50 μl reaction solution, using a GeneAmp PCR System 9700 (Applied Biosystems, Life Technologies) thermal cycler. .. After pre-heating the PCR solution at 96°C for 4 min, 25 cycles of thermal denaturation/annealing/polymerization steps were performed (10 s at 98°C, 10 s at 50°C and 60 s at 72°C, respectively).

Combined Bisulfite Restriction Analysis Assay:

Article Title: Histone deacetylase regulates insulin signaling via two pathways in pancreatic β cells
Article Snippet: Paragraph title: DNA bisulfite modification, combined bisulfite restriction analysis (COBRA), and direct sequencing ... For methylation-specific PCR, bisulfite-modified DNA (2 μL) was amplified in a volume of 20 μL using specific primers targeting the Irs2 gene (including the transcription factor binding sites) and 1 U of Ex Taq DNA Polymerase Hot-Start Version (TaKaRa), according to the manufacturer’s instructions.

Methylation:

Article Title: Histone deacetylase regulates insulin signaling via two pathways in pancreatic β cells
Article Snippet: Bisulfite treatment of DNA was performed using an EpiTect Bisulfite Kit (QIAGEN) according to the manufacturer’s instructions. .. For methylation-specific PCR, bisulfite-modified DNA (2 μL) was amplified in a volume of 20 μL using specific primers targeting the Irs2 gene (including the transcription factor binding sites) and 1 U of Ex Taq DNA Polymerase Hot-Start Version (TaKaRa), according to the manufacturer’s instructions. .. The primer sequences were 5′-GGGAATTTGATAAGTGAATGG-3′ and 5′-TCCCACTAACTAACCCCAAA-3′.

Size-exclusion Chromatography:

Article Title: Caution for simple sequence repeat number variation in the mitochondrial DNA D-loop to determine cancer-specific variants
Article Snippet: PCR was performed in 20-µl reactions using Takara EX Taq DNA polymerase Hot Start Version (Takara Bio Inc., Shiga, Japan) and KOD-Plus-Neo (Toyobo, Osaka, Japan) according to the manufacturer's instructions. .. The former is a mixture of recombinant Taq DNA polymerase and 3′-5′ exonuclease, and the latter is an enzyme possessing 3′-5′ exonuclease activity; this enzyme is derived from the KOD1 strain of Thermococcus kodakaraensis and as described in the manufacturer's instructions, has 80-fold fidelity compared to recombinant Taq DNA polymerase.

Article Title: Polymorphism-specific PCR enhances the diagnostic performance of American tegumentary leishmaniasis and allows the rapid identification of Leishmania species from Argentina
Article Snippet: Reaction B was performed with the primers M1-M2 for the detection of L. mexicana and L. donovani complexes belonging to the Leishmania subgenus [ ], under the following conditions: initial denaturation at 94°C for five minutes, 35 cycles (30 sec at 94°C, one minute at 60°C, one minute at 72°C), and a final extension step at 72°C for seven minutes) [ ]. .. Additional experiments to control the DNA preparation procedure, as well as to detect the presence of PCR inhibitors were performed using the TaKaRa Ex Taq DNA polymerase Hot Start Version (Takara-Bio, Shiga, Japan) and specific primers for the human glyceraldehydes 3-phosphate dehydrogenase (GAPDH ) gene, following a previously reported protocol [ ].

Purification:

Article Title: Functional characterization of Aquaporin-like genes in the human bed bug Cimex lectularius
Article Snippet: The clones used for full-length sequencing were used for PCR amplification by Ex Taq polymerase Hot Start Version (TaKaRa, Mountain View, CA). .. The clones used for full-length sequencing were used for PCR amplification by Ex Taq polymerase Hot Start Version (TaKaRa, Mountain View, CA).

Article Title: Squalene Cyclases and Cycloartenol Synthases from Polystichum polyblepharum and Six Allied Ferns
Article Snippet: PCR was performed using Ex Taq DNA polymerase Hot Start Version (TaKaRa Bio, Shiga, Japan) in a final volume of 50 μL PCR conditions were identical to those reported in our previous study [ ]. .. The primer-specific amplicon was purified from an agarose gel, cloned into pT7 Blue T-Vector (Merck KGaA, Darmstadt, Germany), and transformed into E. coli strain DH5α.

Article Title: Histone deacetylase regulates insulin signaling via two pathways in pancreatic β cells
Article Snippet: For methylation-specific PCR, bisulfite-modified DNA (2 μL) was amplified in a volume of 20 μL using specific primers targeting the Irs2 gene (including the transcription factor binding sites) and 1 U of Ex Taq DNA Polymerase Hot-Start Version (TaKaRa), according to the manufacturer’s instructions. .. For direct sequencing, bisulfite-modified DNA was amplified using the primers for COBRA analysis and separated on 2.0% agarose gels.

Article Title: Color Vision Variation as Evidenced by Hybrid L/M Opsin Genes in Wild Populations of Trichromatic Alouatta New World Monkeys
Article Snippet: We carried out PCRs in volumes of 50 μl containing 1.5 units of Ex Taq polymerase hot start version (Takara Biotechnology Co., Tokyo, Japan) with 1× Ex Taq buffer, 0.2 mM dNTPs, 2.0 mM MgCl2 , 1 μM forward and reverse primers, and 5 μl of the DNA extract from feces. .. We set cycles at 94°C for 5 min followed by 40 cycles at 94°C for 30 s, at the annealing temperature indicated in Tables and for 30 s, and at 72°C for 30 s. Pure water was used as the template for the negative control in every reaction.

Article Title: Inferred L/M cone opsin polymorphism of ancestral tarsiers sheds dim light on the origin of anthropoid primates
Article Snippet: PCRs were carried out in volumes of 50 μl containing 1.5 units of Ex Taq polymerase hot start version (Takara, Tokyo, Japan) with 1× Ex Taq Buffer, 0.2 mM of dNTP, 1.5 mM MgCl2 , 1 μM of the forward and reverse primers, and ca 1 ng of the tarsier genomic DNA. .. Cycles were set at 94°C for 5 min followed by 40 cycles at 94°C for 30 s, 62°C for 30 s and 72°C for 30–120 s. Pure water was used as the template for the negative control in every reaction.

Article Title: Gene conversion and purifying selection shape nucleotide variation in gibbon L/M opsin genes
Article Snippet: PCRs were carried out in 25 μl containing 1.5 units of Ex Taq polymerase hot start version (Takara, Tokyo) with 1× Ex Taq Buffer, 0.2 mM each of dNTPs, 1 μM each of the forward and reverse primers, and ca. .. 5 ng of the gibbon genomic DNA at 94°C for 10 min followed by 35 cycles at 94°C for 30 sec, 65°C for 30 sec, and 72°C for 4 min. Distilled water was used as the template for the negative control in every reaction.

Article Title: Solitary Neurocysticercosis Case Caused by Asian Genotype of Taenia solium Confirmed by Mitochondrial DNA Analysis
Article Snippet: Serological confirmation of immunoblots using both purified glycoproteins ( ) and a recombinant chimeric antigen ( ) was carried out at Asahikawa Medical College before surgical operation; however, there was no detectable specific antibody response against either antigen (data not shown). .. The PCR protocol consisted of 35 cycles of 94°C for 1 min, 60°C for 1 min, and 72°C for 2 min plus 1 cycle of 72°C for 5 min using the Ex Taq DNA polymerase Hot Start version (Takara Bio Inc., Shiga, Japan).

Reverse Transcription Polymerase Chain Reaction:

Article Title: Raspberry Ketone Promotes the Differentiation of C3H10T1/2 Stem Cells into Osteoblasts
Article Snippet: Paragraph title: Reverse transcription–polymerase chain reaction assay ... One microliter of the product was used for polymerase chain reaction (PCR) amplification in a total volume of 25 μ L containing 1× Taq reaction buffer, 0.2 mM dNTPs, 2 mM MgCl2 , 1 μ M of each primer, and 0.5 U of Takara Ex Taq ® polymerase Hot Start Version (Takara, Otsu, Japan).

shRNA:

Article Title: The positive feedback loop between ILF3 and lncRNA ILF3-AS1 promotes melanoma proliferation, migration, and invasion
Article Snippet: The complementary DNA encoding ILF3 was PCR-amplified by the Ex Taq DNA polymerase hot-start version (Takara) and subcloned into the Nhe I and Kpn I sites of pcDNA3.1(+) plasmid (Thermo Fisher Scientific). .. The empty plasmid pcDNA3.1(+) was used as negative control.

Blocking Assay:

Article Title: Solitary Neurocysticercosis Case Caused by Asian Genotype of Taenia solium Confirmed by Mitochondrial DNA Analysis
Article Snippet: The PCR protocol consisted of 35 cycles of 94°C for 1 min, 60°C for 1 min, and 72°C for 2 min plus 1 cycle of 72°C for 5 min using the Ex Taq DNA polymerase Hot Start version (Takara Bio Inc., Shiga, Japan). .. The PCR protocol consisted of 35 cycles of 94°C for 1 min, 60°C for 1 min, and 72°C for 2 min plus 1 cycle of 72°C for 5 min using the Ex Taq DNA polymerase Hot Start version (Takara Bio Inc., Shiga, Japan).

Lysis:

Article Title: A new species of the genus Arrup from a limestone cave in Akiyoshi-dai, Western Japan ( Chilopoda, Geophilomorpha, Mecistocephalidae)
Article Snippet: The PCR amplification was performed in a Thermal Cycler Dice (Takara) in a 10 μl volume containing 0.5 μl of template solution, 2 mM MgCl2 , 2.5 mM each dNTP, 10 pmol each primer, and 0.25 U Ex Taq polymerase Hot Start version (Takara) in 1× buffer provided by the manufacturer. .. The PCR amplification was performed in a Thermal Cycler Dice (Takara) in a 10 μl volume containing 0.5 μl of template solution, 2 mM MgCl2 , 2.5 mM each dNTP, 10 pmol each primer, and 0.25 U Ex Taq polymerase Hot Start version (Takara) in 1× buffer provided by the manufacturer.

Nested PCR:

Article Title: Squalene Cyclases and Cycloartenol Synthases from Polystichum polyblepharum and Six Allied Ferns
Article Snippet: Homology-based nested PCR was performed using the single-strand cDNA and five degenerate primers [ , ] (SC-306S-1, SC-306S-2, SC-358S, SC-494A, and SC-537A). .. PCR was performed using Ex Taq DNA polymerase Hot Start Version (TaKaRa Bio, Shiga, Japan) in a final volume of 50 μL PCR conditions were identical to those reported in our previous study [ ].

Plasmid Preparation:

Article Title: Squalene Cyclases and Cycloartenol Synthases from Polystichum polyblepharum and Six Allied Ferns
Article Snippet: PCR was performed using Ex Taq DNA polymerase Hot Start Version (TaKaRa Bio, Shiga, Japan) in a final volume of 50 μL PCR conditions were identical to those reported in our previous study [ ]. .. The primer-specific amplicon was purified from an agarose gel, cloned into pT7 Blue T-Vector (Merck KGaA, Darmstadt, Germany), and transformed into E. coli strain DH5α.

Article Title: The positive feedback loop between ILF3 and lncRNA ILF3-AS1 promotes melanoma proliferation, migration, and invasion
Article Snippet: After three times of washes, the membranes were incubated with horseradish peroxidase-conjugated goat antimouse or goat antirabbit secondary antibody (Abcam) and detected using the enhanced chemiluminescence. .. The complementary DNA encoding ILF3 was PCR-amplified by the Ex Taq DNA polymerase hot-start version (Takara) and subcloned into the Nhe I and Kpn I sites of pcDNA3.1(+) plasmid (Thermo Fisher Scientific). .. The sequences of primers were as follows: 5′-CTAGCTAGCGATAAGCAAAAGTTTGATTTCCAG-3′ (sense) and 5′-GGGGTACCGGAGTAAGTGCAGAAGGTAGA-3′ (anti-sense).

Negative Control:

Article Title: The positive feedback loop between ILF3 and lncRNA ILF3-AS1 promotes melanoma proliferation, migration, and invasion
Article Snippet: The complementary DNA encoding ILF3 was PCR-amplified by the Ex Taq DNA polymerase hot-start version (Takara) and subcloned into the Nhe I and Kpn I sites of pcDNA3.1(+) plasmid (Thermo Fisher Scientific). .. The complementary DNA encoding ILF3 was PCR-amplified by the Ex Taq DNA polymerase hot-start version (Takara) and subcloned into the Nhe I and Kpn I sites of pcDNA3.1(+) plasmid (Thermo Fisher Scientific).

Article Title: Polymorphism-specific PCR enhances the diagnostic performance of American tegumentary leishmaniasis and allows the rapid identification of Leishmania species from Argentina
Article Snippet: DNA extracted from Leishmania promastigotes cultured in vitro or from confirmed ATL patients was used as a positive control, whereas DNA of eight healthy individuals from non-endemic area (Japanese subjects) or from lesions of non-ATL patients was used as negative control. .. Additional experiments to control the DNA preparation procedure, as well as to detect the presence of PCR inhibitors were performed using the TaKaRa Ex Taq DNA polymerase Hot Start Version (Takara-Bio, Shiga, Japan) and specific primers for the human glyceraldehydes 3-phosphate dehydrogenase (GAPDH ) gene, following a previously reported protocol [ ].

Recombinant:

Article Title: Solitary Neurocysticercosis Case Caused by Asian Genotype of Taenia solium Confirmed by Mitochondrial DNA Analysis
Article Snippet: Serological confirmation of immunoblots using both purified glycoproteins ( ) and a recombinant chimeric antigen ( ) was carried out at Asahikawa Medical College before surgical operation; however, there was no detectable specific antibody response against either antigen (data not shown). .. The PCR protocol consisted of 35 cycles of 94°C for 1 min, 60°C for 1 min, and 72°C for 2 min plus 1 cycle of 72°C for 5 min using the Ex Taq DNA polymerase Hot Start version (Takara Bio Inc., Shiga, Japan).

Agarose Gel Electrophoresis:

Article Title: Functional characterization of Aquaporin-like genes in the human bed bug Cimex lectularius
Article Snippet: The clones used for full-length sequencing were used for PCR amplification by Ex Taq polymerase Hot Start Version (TaKaRa, Mountain View, CA). .. The clones used for full-length sequencing were used for PCR amplification by Ex Taq polymerase Hot Start Version (TaKaRa, Mountain View, CA).

Article Title: Gene conversion and purifying selection shape nucleotide variation in gibbon L/M opsin genes
Article Snippet: PCRs were carried out in 25 μl containing 1.5 units of Ex Taq polymerase hot start version (Takara, Tokyo) with 1× Ex Taq Buffer, 0.2 mM each of dNTPs, 1 μM each of the forward and reverse primers, and ca. .. 5 ng of the gibbon genomic DNA at 94°C for 10 min followed by 35 cycles at 94°C for 30 sec, 65°C for 30 sec, and 72°C for 4 min. Distilled water was used as the template for the negative control in every reaction.

Article Title: Raspberry Ketone Promotes the Differentiation of C3H10T1/2 Stem Cells into Osteoblasts
Article Snippet: One microliter of the product was used for polymerase chain reaction (PCR) amplification in a total volume of 25 μ L containing 1× Taq reaction buffer, 0.2 mM dNTPs, 2 mM MgCl2 , 1 μ M of each primer, and 0.5 U of Takara Ex Taq ® polymerase Hot Start Version (Takara, Otsu, Japan). .. The primers for α 1(I) collagen, osteocalcin, transforming growth factor β s (TGF- β 1, TGF- β 2, and TGF- β 3), and BMP-2 were synthesized by referring to already published articles., β -Actin was used as the housekeeping gene as an endogenous control.

In Vitro:

Article Title: Functional characterization of Aquaporin-like genes in the human bed bug Cimex lectularius
Article Snippet: The clones used for full-length sequencing were used for PCR amplification by Ex Taq polymerase Hot Start Version (TaKaRa, Mountain View, CA). .. The clones used for full-length sequencing were used for PCR amplification by Ex Taq polymerase Hot Start Version (TaKaRa, Mountain View, CA).

Article Title: Polymorphism-specific PCR enhances the diagnostic performance of American tegumentary leishmaniasis and allows the rapid identification of Leishmania species from Argentina
Article Snippet: DNA extracted from Leishmania promastigotes cultured in vitro or from confirmed ATL patients was used as a positive control, whereas DNA of eight healthy individuals from non-endemic area (Japanese subjects) or from lesions of non-ATL patients was used as negative control. .. Additional experiments to control the DNA preparation procedure, as well as to detect the presence of PCR inhibitors were performed using the TaKaRa Ex Taq DNA polymerase Hot Start Version (Takara-Bio, Shiga, Japan) and specific primers for the human glyceraldehydes 3-phosphate dehydrogenase (GAPDH ) gene, following a previously reported protocol [ ].

Chromosome Walking:

Article Title: Color Vision Variation as Evidenced by Hybrid L/M Opsin Genes in Wild Populations of Trichromatic Alouatta New World Monkeys
Article Snippet: We sequenced the intron 2 to determine the nucleotide haplotypes encompassing exon 2 through exon 3 in one of the three Alouatta palliata (CG-17) by “primer walking” with a series of overlapping PCR amplifications (Table and Fig. ). .. We carried out PCRs in volumes of 50 μl containing 1.5 units of Ex Taq polymerase hot start version (Takara Biotechnology Co., Tokyo, Japan) with 1× Ex Taq buffer, 0.2 mM dNTPs, 2.0 mM MgCl2 , 1 μM forward and reverse primers, and 5 μl of the DNA extract from feces.

Spectrophotometry:

Article Title: Histone deacetylase regulates insulin signaling via two pathways in pancreatic β cells
Article Snippet: The quality and quantity of genomic DNA was assessed using a NanoDrop ND1000 spectrophotometer (Thermo Scientific). .. For methylation-specific PCR, bisulfite-modified DNA (2 μL) was amplified in a volume of 20 μL using specific primers targeting the Irs2 gene (including the transcription factor binding sites) and 1 U of Ex Taq DNA Polymerase Hot-Start Version (TaKaRa), according to the manufacturer’s instructions.

DNA Purification:

Article Title: Color Vision Variation as Evidenced by Hybrid L/M Opsin Genes in Wild Populations of Trichromatic Alouatta New World Monkeys
Article Snippet: We carried out PCRs in volumes of 50 μl containing 1.5 units of Ex Taq polymerase hot start version (Takara Biotechnology Co., Tokyo, Japan) with 1× Ex Taq buffer, 0.2 mM dNTPs, 2.0 mM MgCl2 , 1 μM forward and reverse primers, and 5 μl of the DNA extract from feces. .. We set cycles at 94°C for 5 min followed by 40 cycles at 94°C for 30 s, at the annealing temperature indicated in Tables and for 30 s, and at 72°C for 30 s. Pure water was used as the template for the negative control in every reaction.

Article Title: Inferred L/M cone opsin polymorphism of ancestral tarsiers sheds dim light on the origin of anthropoid primates
Article Snippet: PCRs were carried out in volumes of 50 μl containing 1.5 units of Ex Taq polymerase hot start version (Takara, Tokyo, Japan) with 1× Ex Taq Buffer, 0.2 mM of dNTP, 1.5 mM MgCl2 , 1 μM of the forward and reverse primers, and ca 1 ng of the tarsier genomic DNA. .. Cycles were set at 94°C for 5 min followed by 40 cycles at 94°C for 30 s, 62°C for 30 s and 72°C for 30–120 s. Pure water was used as the template for the negative control in every reaction.

Gel Extraction:

Article Title: Histone deacetylase regulates insulin signaling via two pathways in pancreatic β cells
Article Snippet: For methylation-specific PCR, bisulfite-modified DNA (2 μL) was amplified in a volume of 20 μL using specific primers targeting the Irs2 gene (including the transcription factor binding sites) and 1 U of Ex Taq DNA Polymerase Hot-Start Version (TaKaRa), according to the manufacturer’s instructions. .. For direct sequencing, bisulfite-modified DNA was amplified using the primers for COBRA analysis and separated on 2.0% agarose gels.

Article Title: Changes in Variable Number of Tandem Repeats in ‘Candidatus Liberibacter asiaticus’ through Insect Transmission
Article Snippet: PCR was performed using a GeneAmp PCR System 9700 (Applied Biosystems, Foster City, CA, USA) in a 20-μL reaction mixture containing 1 μL of DNA template, 0.1 μM of each primer, 200 μM dNTP mixture, 1× PCR buffer, and 2.5 units of Ex Taq DNA polymerase Hot Start Version (TaKaRa, Shiga, Japan). .. The thermal cycling conditions were as follows: initial denaturation at 92°C for 2 min; 35 cycles of denaturing at 92°C for 30 s, annealing at 54°C for 30 s, and extension at 72°C for 1 min. Amplified PCR products were separated by electrophoresis in a 1.5% (wt/vol) agarose gel in Tris-boric acid EDTA buffer.

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    TaKaRa ex taq dna polymerase hot start version
    Sequencing electropherogram of (CA)7 . PCR of the mtDNA D-loop (CA)7 was performed using EX <t>Taq</t> <t>DNA</t> polymerase and F7/R5 primer pairs (A) or F5/R5 primer pairs (B). The sequencing electropherogram using the F5 primer is the same as (data not shown). (C) PCR was performed using a different proofreading DNA polymerase KOD and F7/R5 primer pairs. (D) PCR of genomic (CA)7 of the NAALAD2 gene was performed using EX Taq DNA polymerase. An arrow indicates a representative position used to evaluate a variant allele. PCR, polymerase chain reaction; mtDNA, mitochondrial DNA; NB, normal breast epithelia; NLN, normal lymph node; BC, breast cancer; NL16, normal liver; F, forward; R, reverse. NL16 is a different patient with a (CA)4 repeat.
    Ex Taq Dna Polymerase Hot Start Version, supplied by TaKaRa, used in various techniques. Bioz Stars score: 94/100, based on 26 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    TaKaRa taq polymerase
    Sequencing electropherogram of (CA)7 . PCR of the mtDNA D-loop (CA)7 was performed using EX <t>Taq</t> <t>DNA</t> polymerase and F7/R5 primer pairs (A) or F5/R5 primer pairs (B). The sequencing electropherogram using the F5 primer is the same as (data not shown). (C) PCR was performed using a different proofreading DNA polymerase KOD and F7/R5 primer pairs. (D) PCR of genomic (CA)7 of the NAALAD2 gene was performed using EX Taq DNA polymerase. An arrow indicates a representative position used to evaluate a variant allele. PCR, polymerase chain reaction; mtDNA, mitochondrial DNA; NB, normal breast epithelia; NLN, normal lymph node; BC, breast cancer; NL16, normal liver; F, forward; R, reverse. NL16 is a different patient with a (CA)4 repeat.
    Taq Polymerase, supplied by TaKaRa, used in various techniques. Bioz Stars score: 75/100, based on 0 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/taq polymerase/product/TaKaRa
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    taq polymerase - by Bioz Stars, 2019-12
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    Sequencing electropherogram of (CA)7 . PCR of the mtDNA D-loop (CA)7 was performed using EX Taq DNA polymerase and F7/R5 primer pairs (A) or F5/R5 primer pairs (B). The sequencing electropherogram using the F5 primer is the same as (data not shown). (C) PCR was performed using a different proofreading DNA polymerase KOD and F7/R5 primer pairs. (D) PCR of genomic (CA)7 of the NAALAD2 gene was performed using EX Taq DNA polymerase. An arrow indicates a representative position used to evaluate a variant allele. PCR, polymerase chain reaction; mtDNA, mitochondrial DNA; NB, normal breast epithelia; NLN, normal lymph node; BC, breast cancer; NL16, normal liver; F, forward; R, reverse. NL16 is a different patient with a (CA)4 repeat.

    Journal: Oncology Letters

    Article Title: Caution for simple sequence repeat number variation in the mitochondrial DNA D-loop to determine cancer-specific variants

    doi: 10.3892/ol.2018.9809

    Figure Lengend Snippet: Sequencing electropherogram of (CA)7 . PCR of the mtDNA D-loop (CA)7 was performed using EX Taq DNA polymerase and F7/R5 primer pairs (A) or F5/R5 primer pairs (B). The sequencing electropherogram using the F5 primer is the same as (data not shown). (C) PCR was performed using a different proofreading DNA polymerase KOD and F7/R5 primer pairs. (D) PCR of genomic (CA)7 of the NAALAD2 gene was performed using EX Taq DNA polymerase. An arrow indicates a representative position used to evaluate a variant allele. PCR, polymerase chain reaction; mtDNA, mitochondrial DNA; NB, normal breast epithelia; NLN, normal lymph node; BC, breast cancer; NL16, normal liver; F, forward; R, reverse. NL16 is a different patient with a (CA)4 repeat.

    Article Snippet: PCR was performed in 20-µl reactions using Takara EX Taq DNA polymerase Hot Start Version (Takara Bio Inc., Shiga, Japan) and KOD-Plus-Neo (Toyobo, Osaka, Japan) according to the manufacturer's instructions.

    Techniques: Sequencing, Polymerase Chain Reaction, Variant Assay